Right click to open Pop-up-menu > Select 'Surfaces' Scroll down > Click on ' Make Opaque'Ĭhoose Surfaces and select Make Opaque option. We can also make the surfaces opaque or translucent. So, open the Pop-up menu again, and choose Dot Surface. Let us change it to another surface, say, Dot Surface. The model of Benzene is displayed with a molecular surface. Now, right-click on the panel, to open the Pop-up menu.įor demonstration purpose, I will select Molecular surface. To view different surfaces, open the pop-up menu.Įnsure that the modelkit menu is closed, if it is open. Surface topology of the molecules can be displayed by using Jmol Application. Next, we need to introduce two more double bonds in the structure, to convert it to benzene.Ĭlick on the bond between next two carbon atoms > Repeat the above step.Ĭlick on the bond between the next two alternate carbon atoms.ĭo the energy minimization to get a stable conformation. Place the cursor on the bond between any two carbon atoms and click on it. We have to introduce double bonds at alternate positions in the cyclohexane ring.Ĭlick on the bond between two carbon atoms. Let us now convert cyclohexane to a benzene ring. Now Let us go back to the Jmol panel with the model of cyclohexane. We have a model of cyclopentane on the panel. Without releasing the mouse button, bring the cursor to the carbon present at the other end of the chain. Place the cursor on the carbon present at one end of the chain.īring the cursor to other end of the chain and click on the carbon. To convert this into cyclopentane, select Drag to bond option from the modelkit menu. Open modelkit menu and check against Drag to bond option. Open new Jmol window with pentane structure. I will use a model of pentane to demonstrate this feature. Open modelkit menu and scroll down to Drag to bond option.Īlternately, we can also use Drag to bond option in modelkit menu to create cyclic structures. The model of Cyclohexane is now, in its most stable “ chair” conformation. ![]() Use minimize option in the modelkit menu to optimize the structure. This is the structure of butane on the panel.Ĭlick on hydrogen at the end of the chain.Ĭlick on hydrogen on any of the carbon atoms present at the end of the chain.Ĭlick on one of the hydrogens, that is close to the end of the carbon chain.Ī model of cyclohexane is created on the panel.Ĭlick on minimize option in the modelkit menu Now, rotate the structure on screen using the Rotate molecule tool. Repeat this step another 2 times and replace one hydrogen at a time with a methyl group.Ĭlick on the hydrogens in such a way that the structure forms a circle.Ĭlick on Rotate molecule tool and rotate the model. To do so, we will place the cursor on the hydrogen and click on it.Ĭursor on the Ethane molecule > Click on hydrogen. We will substitute the hydrogen in the model with a methyl group. To create cyclohexane, we have to make a hydrocarbon chain of six carbon atoms. ![]() Let us first create a model of cyclohexane.Ĭlick on the modelkit icon in the tool bar I have opened a new Jmol application window. If not, watch the relevant tutorials available at our website. ![]() To follow this tutorial, you should know how to create and edit molecular models in Jmol Application.
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